mbf_gtf
Possibly the fastes Ensembl-GTF parser around (reads the 1GB human GTF in about 10s on my system).
Usage: mbf_gtf.parse_ensembl_gtf("filename.gtf", []) -> A dict of DataFrames
The file may be compressed with gzip - it must then end with ".gz".
The second parameter may be a list of 'features' to retrieve - getting just a subset can greatly improve performance.
Note that this is very ensembl specific, it does not deal with any other GTF format, and that it throws away attributes that are repeated on the sub elements - ie. exons have only gene_id, not gene_name, gene_version, gene_....
The resulting coordinates are pythonic - ie. starting at 0 (ie. shifted -1 from the values in the GTF).
This is part of the mbf_* family of bioinformatic libraries.
1 maintainer
Release files for mbf-gtf 0.6.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| mbf_gtf-0.6.0.tar.gz | 10.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mbf_gtf-0.6.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.8 | abi3 | Linux glibc 2.17+ x86-64 | Details |
Total release size: 344.9 kB
Release files / mbf_gtf-0.6.0.tar.gz
| Download URL | mbf_gtf-0.6.0.tar.gz |
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| Size | 10.3 kB |
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Release files / mbf_gtf-0.6.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | mbf_gtf-0.6.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 334.6 kB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 abi3 |
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